- Modern plant pathology benefits from integrating methods and concepts from evolutionary biology. For example, evolutionary concepts are used to identify and examine species boundaries of plant pathogens, recognize processes underlying pathogen biogeography, identify traits that characterize emerging species, and discover new molecular interactions that originate under processes of selection. In this dissertation, I integrate the elements of evolutionary biology, genomics, computational biology, and plant pathology with the objective of studying the evolutionary dynamics of two species of Phytophthora: P. rubi and P. fragariae, two important pathogens of Rosaceae species. P. rubi is found in the western U.S., where the majority of the fresh and processed raspberries are produced. Root rot of raspberries is one of the most destructive diseases in the western U.S., where up to 90% of the fields surveyed in Washington are affected by this disease. P. fragariae has been a very important disease of Strawberry across the world, and its recognized as the causal agent of red stele of strawberry.
My main objective was to identify the evolutionary dynamics of these species by studying the population structure and migrations of P. rubi across the states of California, Washington and Oregon, the highest producers of red raspberry in the world (Chapter 4). We used genotyping-by-sequencing (GBS) to characterize genetic diversity in populations of P. rubi sampled in the U.S. and other countries. Our results showed no evidence for population differentiation at a global or regional level. This effort also provides evidence of high rates of migration among fields in California and Oregon into Washington. This report provides new insights into the evolution and structure of global and U.S. West coast populations of the raspberry pathogen P. rubi indicating that human activity might be involved in moving the pathogen among regions and fields.
I was also interested in identifying the genomic changes associated with host specificity between P. rubi and P. fragariae to identify the regions of the genomes with evidence of selective pressures (Chapter 5 and Chapter 7). We sequenced the genome and the transcriptome of both species and predicted 23,475 and 20,448 genes for P. fragariae and P. rubi, respectively. Based on resequencing we further screened for evidence of selection and high allele fixation across all pairs of orthologous genes in both species. We found that classic families of genes involved in physiological disruption of the host plant (effectors) show few signatures of positive selection. We observed signatures of selection and selective sweeps in 42 candidate genes. None of these candidate genes are effectors, but rather, are genes involved in processes of transport, signaling, defense, and cell wall degradation, indicating that selection is acting on genes involved in recognition rather than pathogenicity. Therefore, we propose an alternate hypothesis of genome evolution based on a
system of genes involved in processes of recognition of the host, signaling, defense, and breakage of the host cell wall.
Finally, I created bioinformatic tools to facilitate the integration of evolutionary concepts (e.g., species identification. Chapter 2) or the identification of genes of interest (e.g., effector proteins. Chapter 6) for the plant pathology community, and we explore the use of leading genotyping techniques (e.g., genotyping-by-sequencing, Chapter 3) to study the dynamics of populations of plant pathogens. Overall, this dissertation presents an integration of concepts and tools plant pathology, evolutionary theory, genomics and bioinformatics to address questions relevant to the population history and selective pressures of these important plant pathogenic organisms.